The present invention relates to methods and apparatus for analyzing the spatial distribution of gene expression. Gene expression, the transcription of genetic information from DNA in the nucleus into messenger RNA (mRNA) for translation into a protein, is one of the most critical aspects of gene activity. At present, most gene expression studies can investigate only a small number of genes at high spatial resolution (for example, by in situ mRNA hybridization in tissues using probes to specific genes), or investigate a large number of genes at very poor spatial resolution (for example, using a microarray or next-generation nucleotide sequencing of RNA from a small number of dissected tissue regions).
Many commercial applications and scientific questions of broad interest require expression data for a large number of genes over a spatially resolved region, with a high number of sequences. Such spatial analyses could for example, consider the spatial distribution of gene expression in a tissue formed of multiple cell types, expression in contiguous diseased and non-diseased cells, expression in a tumor mass or neighboring tissues, or across a tissue boundary.